Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium

Mitra, Anirban P.; Angamuthu, Kandavelmani; Nagaraja, Valakunja

doi:10.1016/j.tube.2008.06.004

Cited by 29 publications

(32 citation statements)

References 29 publications

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“…2). Since groESL1 operon has already been described17, its upstream sequence was analyzed for the presence of internal terminators/ pause signals, if any, using GeSTer algorithm (Genome Scanner for Terminators)25. The tool predicted a non-canonical I-shaped, factor-independent terminator T tsaD , downstream of tsaD gene.…”

Section: Resultsmentioning

confidence: 99%

The alr-groEL1 operon in Mycobacterium tuberculosis: an interplay of multiple regulatory elements

Bhat

Pathak

Rao

2017

Sci Rep

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Threonylcarbamoyladenosine is a universally conserved essential modification of tRNA that ensures translational fidelity in cellular milieu. TsaD, TsaB and TsaE are identified as tRNA-A37-threonylcarbamoyl (t6A)-transferase enzymes that have been reconstituted in vitro, in few bacteria recently. However, transcriptional organization and regulation of these genes are not known in any of these organisms. This study describes the intricate architecture of a complex multicistronic alr-groEL1 operon, harboring essential genes, namely tsaD, tsaB, tsaE, groES, groEL1, and alr (required for cell wall synthesis), and rimI encoding an N-α- acetyltransferase in Mycobacterium tuberculosis. Using northern blotting, RT-PCR and in vivo fluorescence assays, genes alr to groEL1 were found to constitute an ~6.3 kb heptacistronic operon with multiple internal promoters and an I-shaped intrinsic hairpin-like cis-regulatory element. A strong promoter PtsaD within the coding sequence of rimI gene is identified in M. tuberculosis, in addition. The study further proposes an amendment in the known bicistronic groESL1 operon annotation by providing evidence that groESL1 is co-transcribed as sub-operon of alr-groEL1 operon. The architecture of alr-groEL1 operon, conservation of the genetic context and a mosaic transcriptional profile displayed under various stress conditions convincingly suggest the involvement of this operon in stress adaptation in M. tuberculosis.

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Section: Resultsmentioning

confidence: 99%

The alr-groEL1 operon in Mycobacterium tuberculosis: an interplay of multiple regulatory elements

Bhat

Pathak

Rao

2017

Sci Rep

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“…Additionally, attempts have been made to elucidate features of RNAP from Mycobacterium species [36], [37], [38] and the transcription elongation rates also appear to vary between different RNAPs [39]. Furthermore, the scarcity of canonical intrinsic terminators and an abundance of non-canonical intrinsic terminators across mycobacteria also suggest differences in the transcription termination machinery [40], [41].…”

Section: Introductionmentioning

confidence: 99%

Mycobacterium tuberculosis Rho Is an NTPase with Distinct Kinetic Properties and a Novel RNA-Binding Subdomain

2014

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Two mechanisms – factor independent and dependent termination – ensure the completion of RNA synthesis in eubacteria. Factor-dependent mechanism relies on the Rho protein to terminate transcription by interacting with RNA polymerase. Although well studied in Escherichia coli, the properties of the Rho homologs from most bacteria are not known. The rho gene is unusually large in genus Mycobacterium and other members of actinobacteria, having ∼150 additional residues towards the amino terminal end. We describe the distinct properties of Rho from Mycobacterium tuberculosis. It is an NTPase with a preference for purine nucleoside triphosphates with kinetic properties different from E. coli homolog and an ability to use various RNA substrates. The N-terminal subdomain of MtbRho can bind to RNA by itself, and appears to contribute to the interaction of the termination factor with RNAs. Furthermore, the interaction with RNA induces changes in conformation and oligomerization of MtbRho.

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“…In addition, four thymine to cytosine mutations were found (Table 1): (i) T -1216143- C in the 3’ non coding region of celA2b (Y980_1090) [29] was present in three isolates (ii) T -4284317- C (Thr237Ala) in the coding region of papA2 (Y980_3820c) was present in one isolate. Sequencing of 13 single-colony isolates from the tenth cycle of intracellular growth yielded 10 isolates having the wild-type genotype and three isolates presenting a single-point mutation.…”

Section: Resultsmentioning

confidence: 99%

Experimental Evolution of Mycobacterium tuberculosis in Human Macrophages Results in Low-Frequency Mutations Not Associated with Selective Advantage

et al. 2016

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Isolates of the human pathogen Mycobacterium tuberculosis recovered from clinical samples exhibit genetic heterogeneity. Such variation may result from the stressful environment encountered by the pathogen inside the macrophage, which is the host cell tubercle bacilli parasitize. To study the evolution of the M. tuberculosis genome during growth inside macrophages, we developed a model of intracellular culture in which bacteria were serially passaged in macrophage-like THP-1 cells for about 80 bacterial generations. Genome sequencing of single bacterial colonies isolated before and after the infection cycles revealed that M. tuberculosis developed mutations at a rate of about 5.7 × 10−9 / bp/ generation, consistent with mutation rates calculated during in vivo infection. Analysis of mutant growth in macrophages and in mice showed that the mutations identified after the cyclic infection conferred no advantage to the mutants relative to wild-type. Furthermore, activity testing of the recombinant protein harboring one of these mutations showed that the presence of the mutation did not affect the enzymatic activity. The serial infection protocol developed in this work to study M. tuberculosis genome microevolution can be applied to exposure to stressors to determine their effect on genome remodeling during intra-macrophage growth.

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Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium

Cited by 29 publications

References 29 publications

The alr-groEL1 operon in Mycobacterium tuberculosis: an interplay of multiple regulatory elements

The alr-groEL1 operon in Mycobacterium tuberculosis: an interplay of multiple regulatory elements

Mycobacterium tuberculosis Rho Is an NTPase with Distinct Kinetic Properties and a Novel RNA-Binding Subdomain

Experimental Evolution of Mycobacterium tuberculosis in Human Macrophages Results in Low-Frequency Mutations Not Associated with Selective Advantage

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